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2005:The Year in Funding


By Jen Crebs and Meredith Salisbury


Remember the funding glory days? You know, back when the NIH budget increased 15 percent or more each year? These days, budgets are tighter than ever. In a survey by Genome Technology this September, 76 percent of readers said grant funding is harder to come by now than it was five or 10 years ago.

One problem in attracting new money is that funding priorities at such large agencies shift, sometimes rapidly; that gene-mapping effort that was valued so highly in the late ’90s couldn’t get anyone’s attention by 2000, when sequencing was the name of the new game. Sixty percent of respondents to our survey say their research has changed in the past five years due to priority shifts at funding agencies.

So it helps to know where the money is, and where it’s going. To that end, GT rounded up all the grant money given out by the major government agencies since the beginning of this year, calling out all of the grants that have to do with the disciplines that comprise systems biology, such as proteomics, sequencing, and so on. Then we sorted through the data to see which fields got the most new money, and which got the least. To add to that information, we polled public-sector readers about lab funding; 402 people took the time to tell us, among other things, which fields they had fled or joined as a result of agency priorities. Taken as a whole, these graphs offer a picture of where the money is right now, as well as which avenues are drying up and which are just starting to open up.

Of course, numbers can never tell the whole story. Survey respondents told us whom they consider the leading grant-getters in their fields — so we got a hold of those people to learn their advice for finding opportunities and writing the best possible grant proposal.

Notes on methodology:

To compile the data for the charts on pages 30 and 35, the GT staff culled the grants databases for the major agencies (DOE did not break out its funding, so it was not included). We then pulled out all of the research grants obviously related to genomics, proteomics, bioinformatics, and the other disciplines that comprise systems biology, deliberately not including grants for lab infrastructure or equipment purchases. Those grants were the basis for the data in these two charts. For the purposes of compiling data for the chart on p. 35, we chose broad technology categories. Genomics includes sequencing, comparative genomics, and DNA structure studies. Proteomics includes mass spec, protein structure and function, and protein-protein interactions. Transcription/pathways also includes cell signaling research. Pharmacogenomics also covers genotyping and disease association studies.


Grantee: Robert Martienssen

Affiliation: Professor, Cold Spring Harbor Laboratory

Major grant: Transposons, RNA Interference and Heterochromatin. This award provides for examining “the proposition that heterochromatin silences genes by virtue of transposon mediated gene regulation, using Arabidopsis thaliana and the fission yeast S. pombe as model systems,” according to Martienssen’s abstract. His team will use genomic tiling microarrays as well as forward and reverse mutagenesis in the effort to better understand the molecular and cytological basis of heterochromatic centromere repeats. This grant was given by the National Institute of General Medical Sciences; it started in 2003 and runs through 2007. In FY 2005, it was worth $339,000.

In his words:

How far in advance should you start writing a grant proposal?

Of course you should start writing at least a month before the deadline, much earlier if there are multiple investigators. But if you have a great idea and the time is right, fundable applications can be written in a week.

How do you find appropriate funding vehicles?

Cold Spring Harbor Laboratory has a terrific sponsored projects office that keeps us up to date.

Do you have any specific tips that have helped your proposals?

Write the “background and significance” section as if it were a review article. I have been known to publish these sections as reviews; grants should be more spontaneous and speculative than papers and can make great reading for “Opinions” and “Trends” review journals.

What are the most common mistakes you’ve seen as a reviewer of grants for this field?

Hesitation, deviation, and repetition. But seriously, making the text too dense and impenetrable is the most common mistake. It should be a pleasure to read, not a challenge, with well-placed figures and well-spaced text. Edit the text on paper, as well as on the computer, to avoid repetition and help with the layout.



Grantee: Richard Gibbs

Affiliation: Professor, Department of Molecular and Human Genetics, Baylor College of Medicine; Director, Human Genome Sequencing Center

Major grant: Large-Scale Sequencing at the Baylor College of Medicine Human Genome Sequencing Center. This NHGRI grant provided for the Baylor center to continue working in the sequencing network, and aims specifically for draft versions of the rhesus macaque and bovine genomes. Additionally, the team will work on improving technology for large-scale genomics — expanding shotgun sequence capabilities and reducing costs, as well as combining the BAC and shotgun approaches and using the Clone Array Pooled Shotgun Sequencing strategy developed in the center. The team will also work on genome finishing methods and submit completed sequence for 10 percent to 15 percent of its sequences. The grant was awarded by NHGRI beginning in 2003 and running through 2006. Funding began at $35 million for FY 2004 and was $32.7 million for FY 2005.

In his words:

How far in advance should you start writing a grant proposal?

Weeks, not months. [The] fastest one I ever wrote was about six hours but it did not get funded.

How do you find appropriate funding vehicles?

I rely on the network of people but I think the Web resources are pretty good now. Any good department has at least one individual who keeps an eye on these things.

Do you have any specific tips that have helped your proposals?

I tell all grant writers ‘hit high and hit low — leave out the middle.’ The document should serve the quick reader who just looks at high points, and should also go deep where there are critical issues.

What are the most common mistakes you’ve seen as a reviewer of grants for this field?

Many make the mistake of going deep where there are not critical issues and leaving out clear overall sections and statements about what the purpose is.

I have a lot of faith in the system: high-quality and thoughtful science does get supported. Applicants should put themselves in the reviewers’ shoes and ask, “Is this high quality; is it precise; is it exciting; is it concisely communicated?”

The very most important thing is that you have to believe in what you are doing — its importance, its value, and its probability of success.


Grantee: John Yates

Affiliation: Professor of Cell Biology, The Scripps Research Institute

Major grant: Proteomic Profiling of CFTR Protein Interaction. This award allows Yates’ team to identify the main protein interactions associated with transport and function in the most common form of cystic fibrosis. The funding will also go toward developing and applying MudPIT, or the methods of quantitative multi-dimensional protein identification technology, and multiple ion reaction monitoring mass spec to define protein interactions. The grant was given by the National Heart, Lung, and Blood Institute in late 2004 and runs through 2009. In FY 2005, it was worth approximately $464,000 to the Yates lab.

In his words:

How far in advance should you start writing a grant proposal?

I like to start at least four weeks [prior]. I have started with as little time as one week — needless to say, that grant didn’t get funded.

How do you find appropriate funding vehicles?

I hear from other people, I check the NIH website, and I watch [for news releases].

Do you have any specific tips that have helped your proposals?

The two things that are probably most important are to be doing state-of-the-art, exciting research, and second, having an ample amount of preliminary data. There’s an adage that you’ve got to have a grant completed in order to get it funded; unfortunately there’s a lot of truth to that.

What are the most common mistakes you’ve seen as a reviewer of grants for this field?

Probably the most common mistakes are grantsmanship issues: being clear and explicit in what you’re going to do and how you’re going to do it. Does the preliminary data support what you are proposing to do? A third is relevance to the topic of the grant.

Science vs. Connections

Researchers whose primary funding comes from NIH, NSF, and USDA agreed that the main factor in winning grant funding was having “a solid scientific proposal with plenty of preliminary data.” Researchers who say their primary funding comes from DOE said the most important factor was being a “well-known or well-connected PI.”


Median annual grant funding by respondents’ major research area

Between $100,000 and $500,000

Gene expression/arrays



Between $500,000 and $1 million




Functional genomics/RNAi


Grantee: George Church

Affiliation: Professor of Genetics, Harvard Medical School; Director, Center for Computational Genetics

Major grant: Molecular and Genomic Imaging Center. This center aims to meet a biomedical need for identifying and characterizing “variation in biological systems at the level of genomes and transcriptomes” by continuing work on the polony (polymerase colony) technology originally developed in Church’s lab, according to the abstract. The primary goals of the grant are: fluorescent in situ sequencing; single-molecule transcriptome profiling; direct haplotyping; single-cell DNA and RNA characterization; and computational algorithms and system modeling for analysis. This grant, awarded by NHGRI as part of its Centers of Excellence in Genomic Science program, began in 2004 at a value of $2 million annually and runs through 2009.

In his words:

How far in advance should you start writing a grant proposal?

Five years if possible, since a key component is “preliminary data.” Also a rush job in the writing means that you will be writing it twice, so you might as well spend twice as much time the first time.

Also, it helps if you have a support group championing a “new” field like “genomics” in 1984 or “synthetic biology” in 2005 lobbying for RFPs.

Do you have any specific tips that have helped your proposals?

There are some that I haven’t learned, but perhaps [others] could learn, like writing beautiful prose with no leaps in thought, clear alternatives if plan A underperforms. Also be creative but down-to-earth realistic (especially when starting). Start with “Why?” Why is this work worth doing? Why is it useful? Why this way rather than another? Why hasn’t it been done before?

What are the most common mistakes you’ve seen as a reviewer of grants for this field?

Unfortunately most of the “mistakes” I see are when someone deserving doesn’t get the grant. This is in part because the system is not designed for [every type of] funding. Rather than nurturing the people who we have supported for years as students and postdocs, a sink-or-swim approach kicks in. It discourages risk-taking pioneers and encourages excess grant writing (and hence extra grant reviewing and lost jobs).



Grantee: David Haussler

Affiliation: Professor, Biomolecular Engineering, University of California, Santa Cruz; Director, Center for Biomolecular Science and Engineering

Major grant: UCSC Center for Genomic Science. This center was designed to provide bioinformatics support and work with what is now the Broad Institute for comparative genomic studies on humans and other vertebrates. Part of the grant enables the center to provide monthly assemblies of the human genome sequence, as well as “an integrated database of links to ESTs, mRNAs, SNPs, gene predictions, markers, isochores, contigs, gaps, clones, and homologies with other vertebrates, mapped to specific positions on the assembled genome and viewable side-by-side on the Web through an interactive browser,” according to the abstract. Other aims include developing new methods for comparative genomics and algorithms and custom array technology to study structure and function of human genes. The grant also covers a 1,000 CPU computer cluster, funding jointly through this award and the Howard Hughes Medical Institute. The NHGRI grant began in 2001 and runs through 2006. In FY 2005, funding was $3.3 million.

In his words:

How far in advance should you start writing a grant proposal?

Three months. But people seldom do. The most important thing is to set a deadline for getting the whole proposal written at least two weeks before it is due, so you have time to get comments from colleagues and make final adjustments before submitting.

How do you find appropriate funding vehicles?


Do you have any specific tips that have helped your proposals?

Write about what excites you. You should be able to put yourself in the place of someone who is not an expert in your particular subfield, hear your prose through their ears, and still understand it and get excited about the ideas. If it is not exciting, then why are you doing it?

The second thing is to have some strong results in the bag before writing the proposal. You need to prove that you have already finished something significant and that the proposed work will go beyond your previous work in a significant way. Half-finished research, if it is discussed at all, should be presented as feasibility studies for the new proposed work — as if it was done as part of the grant proposal preparation process.

What are the most common mistakes you’ve seen as a reviewer of grants for this field?

Personally, I hate it when the applicant doesn’t have a Web interface I can use to explore their previous work.


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